ajpdb.c


Section: Constructors

All constructors return a pointer to a new instance. It is the responsibility of the user to first destroy any previous instance. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions:
ajPdbtospReadAllRawNewReads the swissprot:pdb equivalence table available at URL (1) (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and returns the data as a list of Pdbtosp objects.
ajPdbtospReadNewRead a Pdbtosp object from a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).
ajPdbtospReadCNewRead a Pdbtosp object from a file in embl-like format. Memory for the object is allocated.
ajPdbtospReadAllNewRead all the Pdbtosp objects in a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application) and writes a list of these objects. It then sorts the list by PDB id.
ajCmapReadINewRead a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as an integer. If the arguments mod and chn are both 0, the function will read the next Cmap in the file.
ajCmapReadCNewRead a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as a character.
ajCmapReadAllNewRead every Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application) and returns a list of these objects.
ajCmapReadNewRead a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). This is not usually called by the user, who uses ajCmapReadINew or ajCmapReadCNew instead. If mode==CMAP_MODE_I, chn==0 and mod==0, the function will read the next Cmap in the file.
ajVdwallReadNewRead a Vdwall object from a file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).
ajHetReadNewRead heterogen dictionary, the Het object is allocated.
ajHetReadRawNewReads a dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a Het object.
ajPdbReadFirstModelNewReads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.
ajPdbReadAllModelsNewReads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for all models is read.
ajPdbReadNewReads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.
ajPdbReadoldNewReads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object.
ajPdbReadoldFirstModelNewReads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object. Data for the first model only is read in.
ajAtomNewAtom object constructor. This is normally called by the ajChainNew function.
ajResidueNewResidue object constructor. This is normally called by the ajChainNew function.
ajChainNewChain object constructor. This is normally called by the ajPdbNew function
ajPdbNewPdb object constructor. Fore-knowledge of the number of chains is required. This is normally called by the functions that read PDB files or clean coordinate files (see embpdb.c & embpdbraw.c).
ajHetentNewHetent object constructor.
ajHetNewHet object constructor.
ajVdwallNewVdwall object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of residues is required.
ajVdwresNewVdwres object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of atoms is required.
ajCmapNewCmap object constructor. This is normally called by the ajCmapReadNew function. Fore-knowledge of the dimension (number of residues) for the contact map is required.
ajPdbtospNewPdbtosp object constructor. Fore-knowledge of the number of entries is required. This is normally called by the ajPdbtospReadCNew / ajPdbtospReadNew functions.


Function ajPdbtospReadAllRawNew

Reads the swissprot:pdb equivalence table available at URL (1) (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and returns the data as a list of Pdbtosp objects.

Prototype

AjPList ajPdbtospReadAllRawNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file
AjPList RETURNAJAX List of AJAX PDB to Swiss-Prot (AjPPdbtosp) objects

From EMBOSS 2.9.0


Function ajPdbtospReadNew

Read a Pdbtosp object from a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Prototype

AjPPdbtosp ajPdbtospReadNew (
      AjPFile inf,
      const AjPStr entry
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
const AjPStrentryInputPdb id
AjPPdbtosp RETURNTrue on success

From EMBOSS 2.9.0


Function ajPdbtospReadCNew

Read a Pdbtosp object from a file in embl-like format. Memory for the object is allocated.

Prototype

AjPPdbtosp ajPdbtospReadCNew (
      AjPFile inf,
      const char* entry
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
const char*entryInputPdb id
AjPPdbtosp RETURNTrue on success

From EMBOSS 2.9.0


Function ajPdbtospReadAllNew

Read all the Pdbtosp objects in a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application) and writes a list of these objects. It then sorts the list by PDB id.

Prototype

AjPList ajPdbtospReadAllNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
AjPList RETURNList of Pdbtosp objects.

From EMBOSS 2.9.0


Function ajCmapReadINew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as an integer. If the arguments mod and chn are both 0, the function will read the next Cmap in the file.

Prototype

AjPCmap ajCmapReadINew (
      AjPFile inf,
      ajint chn,
      ajint mod
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
ajintchnInputChain number
ajintmodInputModel number
AjPCmap RETURNPointer to new Cmap object.

From EMBOSS 2.9.0


Function ajCmapReadCNew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as a character.

Prototype

AjPCmap ajCmapReadCNew (
      AjPFile inf,
      char chn,
      ajint mod
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
charchnInputChain number
ajintmodInputModel number
AjPCmap RETURNPointer to new Cmap object.

From EMBOSS 2.9.0


Function ajCmapReadAllNew

Read every Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application) and returns a list of these objects.

Prototype

AjPList ajCmapReadAllNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
AjPList RETURNList of Cmap objects.

From EMBOSS 3.0.0


Function ajCmapReadNew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). This is not usually called by the user, who uses ajCmapReadINew or ajCmapReadCNew instead. If mode==CMAP_MODE_I, chn==0 and mod==0, the function will read the next Cmap in the file.

Prototype

AjPCmap ajCmapReadNew (
      AjPFile inf,
      ajint mode,
      ajint chn,
      ajint mod
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream.
ajintmodeInputMode, either CMAP_MODE_I (treat chn arg as an integer) or CMAP_MODE_C (treat chn arg as a character).
ajintchnInputChain identifier / number.
ajintmodInputModel number.
AjPCmap RETURNTrue on success (an object read)

From EMBOSS 2.9.0


Function ajVdwallReadNew

Read a Vdwall object from a file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Prototype

AjPVdwall ajVdwallReadNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
AjPVdwall RETURNPointer to Vdwall object.

From EMBOSS 2.9.0


Function ajHetReadNew

Read heterogen dictionary, the Het object is allocated.

Prototype

AjPHet ajHetReadNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to Het file
AjPHet RETURNHet object.

From EMBOSS 2.9.0


Function ajHetReadRawNew

Reads a dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a Het object.

Prototype

AjPHet ajHetReadRawNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to dictionary
AjPHet RETURNTrue on success

From EMBOSS 2.9.0


Function ajPdbReadFirstModelNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Prototype

AjPPdb ajPdbReadFirstModelNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to clean coordinate file
AjPPdb RETURNPointer to Pdb object.

From EMBOSS 2.9.0


Function ajPdbReadAllModelsNew

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for all models is read.

Prototype

AjPPdb ajPdbReadAllModelsNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to clean coordinate file
AjPPdb RETURNPointer to Pdb object.

From EMBOSS 3.0.0


Function ajPdbReadNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Prototype

AjPPdb ajPdbReadNew (
      AjPFile inf,
      ajint mode
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to clean coordinate file
ajintmodeInputMode. 0==Read first model only. 1==Read all models.
AjPPdb RETURNPointer to Pdb object.

From EMBOSS 2.9.0


Function ajPdbReadoldNew

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object.

Prototype

AjPPdb ajPdbReadoldNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to clean coordinate file
AjPPdb RETURNPointer to Pdb object.

From EMBOSS 3.0.0


Function ajPdbReadoldFirstModelNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object. Data for the first model only is read in.

Prototype

AjPPdb ajPdbReadoldFirstModelNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to clean coordinate file
AjPPdb RETURNPointer to Pdb object.

From EMBOSS 3.0.0


Function ajAtomNew

Atom object constructor. This is normally called by the ajChainNew function.

Prototype

AjPAtom ajAtomNew (
      void
);

TypeNameRead/WriteDescription
AjPAtom RETURNPointer to an atom object

From EMBOSS 1.8.0


Function ajResidueNew

Residue object constructor. This is normally called by the ajChainNew function.

Prototype

AjPResidue ajResidueNew (
      void
);

TypeNameRead/WriteDescription
AjPResidue RETURNPointer to a Residue object

From EMBOSS 3.0.0


Function ajChainNew

Chain object constructor. This is normally called by the ajPdbNew function

Prototype

AjPChain ajChainNew (
      void
);

TypeNameRead/WriteDescription
AjPChain RETURNPointer to a chain object

From EMBOSS 1.8.0


Function ajPdbNew

Pdb object constructor. Fore-knowledge of the number of chains is required. This is normally called by the functions that read PDB files or clean coordinate files (see embpdb.c & embpdbraw.c).

Prototype

AjPPdb ajPdbNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputNumber of chains in this pdb file
AjPPdb RETURNPointer to a pdb object

From EMBOSS 1.8.0


Function ajHetentNew

Hetent object constructor.

Prototype

AjPHetent ajHetentNew (
      void
);

TypeNameRead/WriteDescription
AjPHetent RETURNPointer to a Hetent object

From EMBOSS 2.9.0


Function ajHetNew

Het object constructor.

Prototype

AjPHet ajHetNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputNumber of entries in dictionary.
AjPHet RETURNPointer to a Het object

From EMBOSS 2.9.0


Function ajVdwallNew

Vdwall object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of residues is required.

Prototype

AjPVdwall ajVdwallNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputNumber of residues
AjPVdwall RETURNPointer to a Vdwall object

From EMBOSS 2.9.0


Function ajVdwresNew

Vdwres object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of atoms is required.

Prototype

AjPVdwres ajVdwresNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputNumber of atoms
AjPVdwres RETURNPointer to a Vdwres object

From EMBOSS 2.9.0


Function ajCmapNew

Cmap object constructor. This is normally called by the ajCmapReadNew function. Fore-knowledge of the dimension (number of residues) for the contact map is required.

Prototype

AjPCmap ajCmapNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputDimension of contact map
AjPCmap RETURNPointer to a Cmap object

From EMBOSS 2.9.0


Function ajPdbtospNew

Pdbtosp object constructor. Fore-knowledge of the number of entries is required. This is normally called by the ajPdbtospReadCNew / ajPdbtospReadNew functions.

Prototype

AjPPdbtosp ajPdbtospNew (
      ajuint n
);

TypeNameRead/WriteDescription
ajuintnInputNumber of entries
AjPPdbtosp RETURNPointer to a Pdbtosp object

From EMBOSS 2.9.0


Section: Destructors

All destructor functions receive the address of the instance to be deleted. The original pointer is set to NULL so is ready for re-use.

Functions:
ajAtomDelDestructor for an AJAX Atom object.
ajResidueDelDestructor for an AJAX Residue object.
ajChainDelDestructor for an AJAX Chain object.
ajPdbDelDestructor for an AJAX PDB object.
ajHetentDelDestructor for an AJAX Hetent object.
ajHetDelDestructor for an AJAX Het object.
ajVdwallDelDestructor for an AJAX Vdwall object.
ajVdwresDelDestructor for an AJAX Vdwres object.
ajCmapDelDestructor for an AJAX Cmap object.
ajPdbtospDelDestructor for an AJAX Pdbtosp object.


Function ajAtomDel

Destructor for an AJAX Atom object.

Prototype

void ajAtomDel (
      AjPAtom* Patom
);

TypeNameRead/WriteDescription
AjPAtom*PatomDeleteAJAX Atom address
void RETURN

From EMBOSS 1.8.0


Function ajResidueDel

Destructor for an AJAX Residue object.

Prototype

void ajResidueDel (
      AjPResidue* Presidue
);

TypeNameRead/WriteDescription
AjPResidue*PresidueDeleteAJAX Residue address
void RETURN

From EMBOSS 3.0.0


Function ajChainDel

Destructor for an AJAX Chain object.

Prototype

void ajChainDel (
      AjPChain* Pchain
);

TypeNameRead/WriteDescription
AjPChain*PchainDeleteAJAX Chain address
void RETURN

From EMBOSS 1.8.0


Function ajPdbDel

Destructor for an AJAX PDB object.

Prototype

void ajPdbDel (
      AjPPdb* Ppdb
);

TypeNameRead/WriteDescription
AjPPdb*PpdbDeleteAJAX PDB address
void RETURN

From EMBOSS 1.8.0


Function ajHetentDel

Destructor for an AJAX Hetent object.

Prototype

void ajHetentDel (
      AjPHetent* Phetent
);

TypeNameRead/WriteDescription
AjPHetent*PhetentDeleteAJAX Hetent address
void RETURN

From EMBOSS 2.9.0


Function ajHetDel

Destructor for an AJAX Het object.

Prototype

void ajHetDel (
      AjPHet* Phet
);

TypeNameRead/WriteDescription
AjPHet*PhetDeleteAJAX Het address
void RETURN

From EMBOSS 2.9.0


Function ajVdwallDel

Destructor for an AJAX Vdwall object.

Prototype

void ajVdwallDel (
      AjPVdwall* Pvdwall
);

TypeNameRead/WriteDescription
AjPVdwall*PvdwallDeleteAJAX Vdwall address
void RETURN

From EMBOSS 2.9.0


Function ajVdwresDel

Destructor for an AJAX Vdwres object.

Prototype

void ajVdwresDel (
      AjPVdwres* Pvdwres
);

TypeNameRead/WriteDescription
AjPVdwres*PvdwresDeleteAJAX Vdwres address
void RETURN

From EMBOSS 2.9.0


Function ajCmapDel

Destructor for an AJAX Cmap object.

Prototype

void ajCmapDel (
      AjPCmap* Pcmap
);

TypeNameRead/WriteDescription
AjPCmap*PcmapDeleteAJAX Cmap address
void RETURN

From EMBOSS 2.9.0


Function ajPdbtospDel

Destructor for an AJAX Pdbtosp object.

Prototype

void ajPdbtospDel (
      AjPPdbtosp* Ppdbtosp
);

TypeNameRead/WriteDescription
AjPPdbtosp*PpdbtospDeleteAJAX Pdbtosp address
void RETURN

From EMBOSS 2.9.0


Section: Assignments

These functions overwrite the instance provided as the first argument A NULL value is always acceptable so these functions are often used to create a new instance by assignment.

Functions:
ajAtomCopyCopies the data from an AJAX Atom object to an AJAX Atom object; the new object is created if needed.
ajResidueCopyCopies the data from a Residue object to an Residue object; the new object is created if needed.
ajAtomListCopyRead a list of Atom structures and writes a copy of the list. The data are copied and the list is created if necessary.
ajResidueListCopyRead a list of Residue structures and writes a copy of the list. The data are copied and the list is created if necessary.
ajPdbCopyCopies data from one AHAX PDB object to another; the new object is always created.


Function ajAtomCopy

Copies the data from an AJAX Atom object to an AJAX Atom object; the new object is created if needed.

Prototype

AjBool ajAtomCopy (
      AjPAtom* Pto,
      const AjPAtom from
);

TypeNameRead/WriteDescription
AjPAtom*PtoOutputAJAX Atom address
const AjPAtomfromInputAJAX Atom
AjBool RETURNTrue on success

From EMBOSS 2.9.0


Function ajResidueCopy

Copies the data from a Residue object to an Residue object; the new object is created if needed.

Prototype

AjBool ajResidueCopy (
      AjPResidue* Pto,
      const AjPResidue from
);

TypeNameRead/WriteDescription
AjPResidue*PtoOutputAJAX Residue address
const AjPResiduefromInputAJAX Residue
AjBool RETURNTrue on success

From EMBOSS 3.0.0


Function ajAtomListCopy

Read a list of Atom structures and writes a copy of the list. The data are copied and the list is created if necessary.

Prototype

AjBool ajAtomListCopy (
      AjPList* Pto,
      const AjPList from
);

TypeNameRead/WriteDescription
AjPList*PtoOutputAJAX List of AJAX Atom objects to write
const AjPListfromInputList of Atom objects to read
AjBool RETURNTrue if list was copied ok.

From EMBOSS 2.9.0


Function ajResidueListCopy

Read a list of Residue structures and writes a copy of the list. The data are copied and the list is created if necessary.

Prototype

AjBool ajResidueListCopy (
      AjPList* to,
      const AjPList from
);

TypeNameRead/WriteDescription
AjPList*toOutputList of Residue objects to write
const AjPListfromInputList of Residue objects to read
AjBool RETURNTrue if list was copied ok.

From EMBOSS 3.0.0


Function ajPdbCopy

Copies data from one AHAX PDB object to another; the new object is always created.

Prototype

AjBool ajPdbCopy (
      AjPPdb* Pto,
      const AjPPdb from
);

TypeNameRead/WriteDescription
AjPPdb*PtoOutputAJAX PDB address
const AjPPdbfromInputAJAX PDB
AjBool RETURNTrue on success

From EMBOSS 2.9.0


Section: Operators

These functions use the contents of an instance but do not make any changes.

Functions:
ajResidueSSEnvAssigns secondary structure environment of an AJAX Residue
ajResidueEnv1Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv2Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv3Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv4Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv5Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv6Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv7Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv8Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv9Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv10Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv11Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv12Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv13Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv14Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv15Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv16Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajPdbGetEStrideTypeReads a Pdb object and writes a string with the secondary structure. The string that is written is the same length as the full-length chain (regardless of whether coordinates for a residue were available or not) therefore it can be indexed into using residue numbers. The string is allocated if necessary. If secondary structure assignment was not available for a residue a '.' is given in the string.


Function ajResidueSSEnv

Assigns secondary structure environment of an AJAX Residue

Prototype

AjBool ajResidueSSEnv (
      const AjPResidue residue,
      char* SEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
char*SEnvOutputCharacter for the Secondary structure environment
AjPFileflogOutputLog file
AjBool RETURNajTrue on success

From EMBOSS 3.0.0


Function ajResidueEnv1

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv1 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv2

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv2 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv3

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv3 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv4

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv4 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv5

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv5 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv6

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv6 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv7

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv7 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv8

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv8 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv9

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv9 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv10

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv10 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv11

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv11 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv12

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv12 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv13

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv13 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv14

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv14 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv15

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv15 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajResidueEnv16

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv16 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

TypeNameRead/WriteDescription
const AjPResidueresidueInputAJAX Residue
charSEnvInputSecondary structure environment code
AjPStr*OEnvOutputCharacter for the overall environment class
AjPFileflogOutputLog file
ajint RETURNNumber of environments

From EMBOSS 3.0.0


Function ajPdbGetEStrideType

Reads a Pdb object and writes a string with the secondary structure. The string that is written is the same length as the full-length chain (regardless of whether coordinates for a residue were available or not) therefore it can be indexed into using residue numbers. The string is allocated if necessary. If secondary structure assignment was not available for a residue a '.' is given in the string.

Prototype

ajint ajPdbGetEStrideType (
      const AjPPdb pdb,
      ajuint chn,
      AjPStr* EStrideType
);

TypeNameRead/WriteDescription
const AjPPdbpdbInputAJAX PDB object
ajuintchnInputChain number
AjPStr*EStrideTypeOutputString to hold secondary structure
ajint RETURNLength (residues) of array that was written or -1 (for an error)

From EMBOSS 2.9.0


Section: Reporters

These functions return the contents of an instance but do not make any changes.

Functions:
ajPdbChnidToNumFinds the chain number for a given chain identifier in a pdb structure
ajPdbtospArrFindPdbidPerforms a binary search for a PDB code over an array of Pdbtosp structures (which of course must first have been sorted). This is a case-insensitive search.


Function ajPdbChnidToNum

Finds the chain number for a given chain identifier in a pdb structure

Prototype

AjBool ajPdbChnidToNum (
      char identifier,
      const AjPPdb pdb,
      ajuint* chn
);

TypeNameRead/WriteDescription
charidentifierInputChain identifier
const AjPPdbpdbInputPdb object
ajuint*chnOutputChain number
AjBool RETURNTrue on success

From EMBOSS 2.9.0


Function ajPdbtospArrFindPdbid

Performs a binary search for a PDB code over an array of Pdbtosp structures (which of course must first have been sorted). This is a case-insensitive search.

Prototype

ajint ajPdbtospArrFindPdbid (
      AjPPdbtosp const* array,
      ajint size,
      const AjPStr identifier
);

TypeNameRead/WriteDescription
AjPPdbtosp const*arrayInputArray of AjOPdbtosp objects
ajintsizeInputSize of array
const AjPStridentifierInputSearch term
ajint RETURNIndex of first Pdbtosp object found with an PDB code matching id, or -1 if id is not found.

From EMBOSS 2.9.0


Section: Input & output

These functions are used for formatted input and output to file.

Functions:
ajPdbWriteAllWrites a clean coordinate file for a protein.
ajPdbWriteSegmentWrites a clean coordinate file for a segment, e.g. a domain. The segment corresponds to a sequence that is passed to the function. In the clean coordinate file, the coordinates are presented as belonging to a single chain. Coordinates for heterogens are NOT written to file.
ajHetWriteWrites the contents of a Het object to file.
ajPdbtospWriteReads a list of Pdbtosp objects, e.g. taken from the swissprot:pdb equivalence table available at URL: (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt) and writes the list out to file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).
ajCmapWriteWrite a Cmap object to file in CON format (see documentation for DOMAINATRIX "contacts" application).
ajPdbExitCleanup of Pdb function internals.


Function ajPdbWriteAll

Writes a clean coordinate file for a protein.

Prototype

AjBool ajPdbWriteAll (
      AjPFile outf,
      const AjPPdb pdb
);

TypeNameRead/WriteDescription
AjPFileoutfOutputOutput file stream
const AjPPdbpdbInputAJAX PDB object
AjBool RETURNTrue on success

From EMBOSS 1.9.0


Function ajPdbWriteSegment

Writes a clean coordinate file for a segment, e.g. a domain. The segment corresponds to a sequence that is passed to the function. In the clean coordinate file, the coordinates are presented as belonging to a single chain. Coordinates for heterogens are NOT written to file.

Prototype

AjBool ajPdbWriteSegment (
      AjPFile outf,
      const AjPPdb pdb,
      const AjPStr segment,
      char chnid,
      const AjPStr domain,
      AjPFile errf
);

TypeNameRead/WriteDescription
AjPFileoutfOutputOutput file stream
const AjPPdbpdbInputPdb object
const AjPStrsegmentInputSequence of segment to print out.
charchnidInputChain id of segment
const AjPStrdomainInputDomain code for segment
AjPFileerrfOutputOutput file stream for error messages
AjBool RETURNTrue on success

From EMBOSS 3.0.0


Function ajHetWrite

Writes the contents of a Het object to file.

Prototype

AjBool ajHetWrite (
      AjPFile outf,
      const AjPHet het,
      AjBool dogrep
);

TypeNameRead/WriteDescription
AjPFileoutfOutputOutput file
const AjPHethetInputAJAX Het
AjBooldogrepInputFlag (True if we are to write 'cnt' element of the Het object to file).
AjBool RETURNTrue on success

From EMBOSS 2.9.0


Function ajPdbtospWrite

Reads a list of Pdbtosp objects, e.g. taken from the swissprot:pdb equivalence table available at URL: (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt) and writes the list out to file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Prototype

AjBool ajPdbtospWrite (
      AjPFile outf,
      const AjPList list
);

TypeNameRead/WriteDescription
AjPFileoutfOutputOutput file
const AjPListlistInputList of Pdbtosp objects
AjBool RETURNTrue of file was written ok.

From EMBOSS 2.9.0


Function ajCmapWrite

Write a Cmap object to file in CON format (see documentation for DOMAINATRIX "contacts" application).

Prototype

AjBool ajCmapWrite (
      AjPFile outf,
      const AjPCmap cmap
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream.
const AjPCmapcmapInputCmap object pointer.
AjBool RETURNTrue on success (object was written successfully)

From EMBOSS 3.0.0


Function ajPdbExit

Cleanup of Pdb function internals.

Prototype

void ajPdbExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 6.1.0